Lac repressor bending the DNA operon. More..
Announcement - Two-Day Workshop:
Practical Protein 3D Structure Visualization and Structural Bioinformatics

Dates have changed:
Group I (filled): Monday June 19 & Thursday June 22, 2017.
Group II (filled): Tuesday June 27 & Friday June 30, 2017.
Each week has the same content, for different groups of participants.
Lederle GRC A210, 9:00 AM - 1:00 PM each day.
University of Massachusetts, Amherst
Limited to 12 participants per group.

taught by Eric Martz (UMass, Amherst)
principal author of FirstGlance in Jmol ( buttons in the journal Nature), MolviZ.Org, team member of Proteopedia.Org, and coauthor of the ConSurf Server.

To register, please email
Bringing your own laptop computer is encouraged (details).
  Enolase (4enl; an enzyme in glycolysis) evolutionary conservation from ConSurf. Catalytic pocket is highly conserved. More..

Level: This course is designed for faculty, postdocs, research staff and graduate students in biological/biochemical sciences. No prior experience with protein 3D visualization or bioinformatics is necessary.
Objectives: Participants will use highly user-friendly software for visual investigation of 3D molecular structures of proteins, nucleic acids, and their interactions with each other and with ligands, substrates, and drugs; and protein evolutionary conservation. Hands-on experience will be largely with molecules of each participant's choosing. We will touch on the challenges of crystallography, uncertainty in electron density maps, and the nature of 3D structure data ("PDB files"). Participants will learn how to create publication-quality molecular images, and presentation-ready animations for Powerpoint slides.

Potassium channel (1R3J) showing membrane surface planes (from OPM).
Participants will gain hands-on experience with:
  • Visual exploration of the 3D structures of macromolecules, such as proteins bound to ligands or nucleic acids.
  • Finding protein structures related to your research, how they are determined, and how much of the proteome has known structure.
  • Obtaining homology models with an automated server (Swiss-Model) when a crystallographic structure is not available.

  • Seeing noncovalent bonds between a ligand and protein, and measuring interatomic distances.
  • Finding sequence numbers or motifs in the 3D model.
  • Locating patches conserved in evolution, and regions of rapid mutation.
  • Visualizing specific oligomers ("biological units"), and their subunit interactions.
  • Evaluating the quality and reliability of a molecular model, and finding gaps in protein chain models.

  • Creating publication-quality molecular images for papers or slides.
  • Creating presentation-ready molecular animations for Powerpoint slides or websites.  See examples

Anti-Alzheimer's drug analog (*) interaction with acetylcholinesterase (1gpk, cf. 1vot: Dvir et al./Sussman, 2002).
Software & Ease of Use: Participants will use powerful, state of the art, free, open-source software designed for ease of use. This software works in web browsers, equally well in Microsoft Windows, Macintosh OS X, or linux, and requires no installation. Learning specialized scripting command language, such as needed for RasMol or PyMol, is not necessary. Most of the resources use Jmol, for which Java is optional.

Computers: Participants should bring their own laptop computers (Windows, Mac OS X, or linux). Mac and Windows computers are also available in the teaching lab. Internet wi-fi & login to lab computers will require a UMass Amherst IT account. Guests should contact to arrange access. Bring your power adaptor: electrical power outlets will be available.

What is Not Covered: Crystallography and model building. Changing molecular models (mutation, energy minimization). Making morph-animations of conformational changes (e.g. lac repressor above left). Professor Martz will be available for private appointments for review, and to help with specific projects or methods not covered in the workshop.

Contents in Detail: For the detailed agenda, please see the course Syllabus.